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Fix issue s1319 Declarations should use Java collection interfaces on biojava-core #1095

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Merged
josemduarte merged 3 commits into from
Jun 17, 2024
Merged

Fix issue s1319 Declarations should use Java collection interfaces on biojava-core #1095

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1ae6b52
Fix issue s1319 Declarations should use Java collection interfaces on…
jlerbsc May 15, 2024
51e125b
Merge branch 'biojava:master' into s1319
jlerbsc Jun 12, 2024
0f4983c
Fix issue s1319 Declarations should use Java collection interfaces on…
jlerbsc Jun 12, 2024
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6 changes: 3 additions & 3 deletions biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
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Expand Up @@ -82,7 +82,7 @@ private static void readInputAndGenerateOutput(String outputLocation, List<Chara
else
output = System.out;
printHeader(output, propertyList, specificList, delimiter);
LinkedHashMap<String, ProteinSequence> a = readInputFile(inputLocation, aaTable);
Map<String, ProteinSequence> a = readInputFile(inputLocation, aaTable);
//Need for the last sequence
for(Entry<String, ProteinSequence> entry:a.entrySet()){
compute(output, entry.getValue().getOriginalHeader(), entry.getValue().getSequenceAsString().trim(), delimiter, aaTable, propertyList, specificList,
Expand Down Expand Up @@ -169,15 +169,15 @@ public static void run(String[] args) throws Exception{
readInputAndGenerateOutput(outputLocation, propertyList, specificList, delimiter, inputLocation, aaTable, decimalPlace);
}

private static LinkedHashMap<String, ProteinSequence> readInputFile(String inputLocation, AminoAcidCompositionTable aaTable) throws Exception{
private static Map<String, ProteinSequence> readInputFile(String inputLocation, AminoAcidCompositionTable aaTable) throws Exception{
FileInputStream inStream = new FileInputStream(inputLocation);
CompoundSet<AminoAcidCompound> set;
if(aaTable == null){
set = CaseFreeAminoAcidCompoundSet.getAminoAcidCompoundSet();
}else{
set = aaTable.getAminoAcidCompoundSet();
}
LinkedHashMap<String, ProteinSequence> ret;
Map<String, ProteinSequence> ret;
if ( inputLocation.toLowerCase().contains(".gb")) {
GenbankReader<ProteinSequence, AminoAcidCompound> genbankReader = new GenbankReader<>(
inStream, new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
Expand Down
3 changes: 2 additions & 1 deletion biojava-alignment/src/main/java/demo/DemoDistanceTree.java
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Expand Up @@ -22,6 +22,7 @@

import java.io.InputStream;
import java.util.LinkedHashMap;
import java.util.Map;

import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
Expand Down Expand Up @@ -64,7 +65,7 @@ public static void main(String[] args) throws Exception {
new ProteinSequenceCreator(AminoAcidCompoundSet
.getAminoAcidCompoundSet()));

LinkedHashMap<String, ProteinSequence> proteinSequences =
Map<String, ProteinSequence> proteinSequences =
fastaReader.process();

inStream.close();
Expand Down
3 changes: 2 additions & 1 deletion biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
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Expand Up @@ -43,6 +43,7 @@
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

public class TestDNAAlignment {

Expand Down Expand Up @@ -75,7 +76,7 @@ public void testDNAAlignment() {
private static List<DNASequence> getDNAFASTAFile() throws Exception {

InputStream inStream = TestDNAAlignment.class.getResourceAsStream(String.format("/dna-fasta.txt"));
LinkedHashMap<String, DNASequence> fastas = FastaReaderHelper.readFastaDNASequence(inStream);
Map<String, DNASequence> fastas = FastaReaderHelper.readFastaDNASequence(inStream);

List<DNASequence> sequences = new ArrayList<DNASequence>();

Expand Down
3 changes: 2 additions & 1 deletion biojava-alignment/src/test/java/org/biojava/nbio/phylo/TestForesterWrapper.java
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Expand Up @@ -24,6 +24,7 @@
import java.io.InputStream;
import java.io.OutputStream;
import java.util.LinkedHashMap;
import java.util.Map;

import org.biojava.nbio.core.sequence.MultipleSequenceAlignment;
import org.biojava.nbio.core.sequence.ProteinSequence;
Expand Down Expand Up @@ -61,7 +62,7 @@ public void testMSAconversion() throws Exception {
new ProteinSequenceCreator(AminoAcidCompoundSet
.getAminoAcidCompoundSet()));

LinkedHashMap<String, ProteinSequence> proteinSequences = fastaReader
Map<String, ProteinSequence> proteinSequences = fastaReader
.process();

inStream.close();
Expand Down
2 changes: 1 addition & 1 deletion biojava-core/src/main/java/demo/DemoSixFrameTranslation.java
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Expand Up @@ -112,7 +112,7 @@ public static void main(String[] args){
new DNASequenceCreator(ambiguityDNACompoundSet));

// has only one entry in this example, but could be easily extended to parse a FASTA file with multiple sequences
LinkedHashMap<String, DNASequence> dnaSequences = proxy.process();
Map<String, DNASequence> dnaSequences = proxy.process();

// Initialize the Transcription Engine
TranscriptionEngine engine = new
Expand Down
4 changes: 3 additions & 1 deletion biojava-core/src/main/java/demo/ParseFastaFileDemo.java
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Expand Up @@ -24,6 +24,8 @@
import java.io.File;
import java.io.InputStream;
import java.util.LinkedHashMap;
import java.util.Map;

import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
Expand Down Expand Up @@ -99,7 +101,7 @@ public static void main(String[] args) throws Exception {
new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));

LinkedHashMap<String, ProteinSequence> b;
Map<String, ProteinSequence> b;

int nrSeq = 0;

Expand Down
5 changes: 3 additions & 2 deletions biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
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Expand Up @@ -27,6 +27,7 @@
import java.util.NoSuchElementException;

import org.biojava.nbio.core.sequence.template.Sequence;
import java.util.Map;

/**
* This class models a search result.
Expand All @@ -46,7 +47,7 @@ public abstract class Result implements Iterable<Hit>{
private String reference;
private String dbFile;

private HashMap<String,String> programSpecificParameters;
private Map<String, String> programSpecificParameters;

private int iterationNumber;
private String queryID;
Expand All @@ -56,7 +57,7 @@ public abstract class Result implements Iterable<Hit>{
private List<Hit> hits;
private int hitCounter = -1;

public Result(String program, String version, String reference, String dbFile, HashMap<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
public Result(String program, String version, String reference, String dbFile, Map<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
this.program = program;
this.version = version;
this.reference = reference;
Expand Down
3 changes: 2 additions & 1 deletion biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
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Expand Up @@ -28,6 +28,7 @@
import java.util.List;
import java.util.ServiceLoader;
import java.util.NoSuchElementException;
import java.util.Map;

/**
* Designed by Paolo Pavan.
Expand All @@ -39,7 +40,7 @@
*/

public class SearchIO implements Iterable<Result>{
static private HashMap<String,ResultFactory> extensionFactoryAssociation;
static private Map<String, ResultFactory> extensionFactoryAssociation;

final private ResultFactory factory;
final private File file;
Expand Down
3 changes: 2 additions & 1 deletion biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResult.java
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Expand Up @@ -25,6 +25,7 @@
import java.util.HashMap;
import java.util.List;
import org.biojava.nbio.core.sequence.template.Sequence;
import java.util.Map;

/**
* This class models a Blast/Blast plus result.
Expand All @@ -39,7 +40,7 @@
*
*/
public class BlastResult extends Result{
public BlastResult(String program, String version, String reference, String dbFile, HashMap<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
public BlastResult(String program, String version, String reference, String dbFile, Map<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
super(program, version, reference, dbFile, programSpecificParameters, iterationNumber, queryID, queryDef, queryLength, hits, querySequence);
}

Expand Down
5 changes: 3 additions & 2 deletions biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.java
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Expand Up @@ -24,6 +24,7 @@
import java.util.HashMap;
import java.util.List;
import org.biojava.nbio.core.sequence.template.Sequence;
import java.util.Map;

/**
* Designed by Paolo Pavan.
Expand All @@ -39,7 +40,7 @@ public class BlastResultBuilder {
private String version;
private String reference;
private String dbFile;
private HashMap<String, String> programSpecificParameters;
private Map<String, String> programSpecificParameters;
private int iterationNumber;
private String queryID;
private String queryDef;
Expand Down Expand Up @@ -70,7 +71,7 @@ public BlastResultBuilder setDbFile(String dbFile) {
return this;
}

public BlastResultBuilder setProgramSpecificParameters(HashMap<String, String> programSpecificParameters) {
public BlastResultBuilder setProgramSpecificParameters(Map<String, String> programSpecificParameters) {
this.programSpecificParameters = programSpecificParameters;
return this;
}
Expand Down
3 changes: 2 additions & 1 deletion biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
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Expand Up @@ -37,6 +37,7 @@
import org.biojava.nbio.core.sequence.template.Sequence;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Map;

/**
* Designed by Paolo Pavan.
Expand Down Expand Up @@ -71,7 +72,7 @@ private enum PARSING_CONSISTENCY {

// data imported private:
int queryIdNumber = 0;
HashMap<String,String> queryIdMapping = new HashMap<>();
Map<String, String> queryIdMapping = new HashMap<>();
String programName=null, queryName = null, databaseFile = null;
private String queryId ;
private String subjectId ;
Expand Down
14 changes: 7 additions & 7 deletions biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
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Expand Up @@ -90,9 +90,9 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
// create mappings between sequences and blast id
mapIds();

ArrayList<Result> resultsCollection;
ArrayList<Hit> hitsCollection;
ArrayList<Hsp> hspsCollection;
List<Result> resultsCollection;
List<Hit> hitsCollection;
List<Hsp> hspsCollection;

try {
// select top level elements
Expand All @@ -102,7 +102,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
String dbFile = XMLHelper.selectSingleElement(blastDoc.getDocumentElement(),"BlastOutput_db").getTextContent();

logger.info("Query for hits in "+ targetFile);
ArrayList<Element> IterationsList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
List<Element> IterationsList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
logger.info(IterationsList.size() + " results");

resultsCollection = new ArrayList<>();
Expand All @@ -129,7 +129,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc


Element iterationHitsElement = XMLHelper.selectSingleElement(element, "Iteration_hits");
ArrayList<Element> hitList = XMLHelper.selectElements(iterationHitsElement, "Hit");
List<Element> hitList = XMLHelper.selectElements(iterationHitsElement, "Hit");

hitsCollection = new ArrayList<>();
for (Element hitElement : hitList) {
Expand All @@ -146,7 +146,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
));

Element hithspsElement = XMLHelper.selectSingleElement(hitElement, "Hit_hsps");
ArrayList<Element> hspList = XMLHelper.selectElements(hithspsElement, "Hsp");
List<Element> hspList = XMLHelper.selectElements(hithspsElement, "Hsp");

hspsCollection = new ArrayList<>();
for (Element hspElement : hspList) {
Expand Down Expand Up @@ -195,7 +195,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc

@Override
public List<String> getFileExtensions(){
ArrayList<String> extensions = new ArrayList<>(1);
List<String> extensions = new ArrayList<>(1);
extensions.add("blastxml");
return extensions;
}
Expand Down
5 changes: 3 additions & 2 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java
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Expand Up @@ -29,6 +29,7 @@
import org.biojava.nbio.core.sequence.template.SequenceReader;

import java.util.LinkedHashMap;
import java.util.Map;

/**
* A ChromosomeSequence is a DNASequence but keeps track of geneSequences
Expand All @@ -37,7 +38,7 @@
public class ChromosomeSequence extends DNASequence {

private int chromosomeNumber;
private LinkedHashMap<String, GeneSequence> geneSequenceHashMap = new LinkedHashMap<>();
private Map<String, GeneSequence> geneSequenceHashMap = new LinkedHashMap<>();

/**
* Empty constructor used by tools that need a proper Bean that allows the actual
Expand Down Expand Up @@ -106,7 +107,7 @@ public void setChromosomeNumber(int chromosomeNumber) {
* @return
*/

public LinkedHashMap<String, GeneSequence> getGeneSequences() {
public Map<String, GeneSequence> getGeneSequences() {
return geneSequenceHashMap;
}

Expand Down
18 changes: 10 additions & 8 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
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Expand Up @@ -32,6 +32,8 @@
import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.List;

/**
*
Expand All @@ -41,11 +43,11 @@ public class GeneSequence extends DNASequence {

private final static Logger logger = LoggerFactory.getLogger(GeneSequence.class);

private final LinkedHashMap<String, TranscriptSequence> transcriptSequenceHashMap = new LinkedHashMap<>();
private final LinkedHashMap<String, IntronSequence> intronSequenceHashMap = new LinkedHashMap<>();
private final LinkedHashMap<String, ExonSequence> exonSequenceHashMap = new LinkedHashMap<>();
private final ArrayList<IntronSequence> intronSequenceList = new ArrayList<>();
private final ArrayList<ExonSequence> exonSequenceList = new ArrayList<>();
private final Map<String, TranscriptSequence> transcriptSequenceHashMap = new LinkedHashMap<>();
private final Map<String, IntronSequence> intronSequenceHashMap = new LinkedHashMap<>();
private final Map<String, ExonSequence> exonSequenceHashMap = new LinkedHashMap<>();
private final List<IntronSequence> intronSequenceList = new ArrayList<>();
private final List<ExonSequence> exonSequenceList = new ArrayList<>();
boolean intronAdded = false; // need to deal with the problem that typically introns are not added when validating the list and adding in introns as the regions not included in exons
private Strand strand = Strand.UNDEFINED;
private ChromosomeSequence chromosomeSequence;
Expand Down Expand Up @@ -179,7 +181,7 @@ public TranscriptSequence getTranscript(String accession) {
* Get the collection of transcription sequences assigned to this gene
* @return transcripts
*/
public LinkedHashMap<String, TranscriptSequence> getTranscripts() {
public Map<String, TranscriptSequence> getTranscripts() {
return transcriptSequenceHashMap;
}

Expand Down Expand Up @@ -294,15 +296,15 @@ public ExonSequence addExon(AccessionID accession, int begin, int end) {
* Get the exons as an ArrayList. Modifying this list will not modify the underlying collection
* @return exons
*/
public ArrayList<ExonSequence> getExonSequences() {
public List<ExonSequence> getExonSequences() {
return new ArrayList<>(exonSequenceList);
}

/**
* Get the introns as an ArrayList. Modifying this list will not modify the underlying collection
* @return introns
*/
public ArrayList<IntronSequence> getIntronSequences() {
public List<IntronSequence> getIntronSequences() {
return new ArrayList<>(intronSequenceList);
}

Expand Down
3 changes: 2 additions & 1 deletion biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
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Expand Up @@ -42,6 +42,7 @@
import java.util.LinkedHashMap;
import java.util.List;
import org.biojava.nbio.core.sequence.features.Qualifier;
import java.util.Map;

/**
* The representation of a ProteinSequence
Expand Down Expand Up @@ -163,7 +164,7 @@ private DNASequence getRawParentSequence(String accessId) throws IOException {
= new FastaReader<>(is,
new PlainFastaHeaderParser<DNASequence, NucleotideCompound>(),
new DNASequenceCreator(AmbiguityDNACompoundSet.getDNACompoundSet()));
LinkedHashMap<String, DNASequence> seq = parentReader.process();
Map<String, DNASequence> seq = parentReader.process();

DNASequence parentSeq = null;
if (seq.size() == 1) {
Expand Down
12 changes: 7 additions & 5 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java
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Expand Up @@ -31,6 +31,8 @@
import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

/**
* This is the sequence if you want to go from a gene sequence to a protein sequence. Need to start with a
Expand All @@ -41,8 +43,8 @@ public class TranscriptSequence extends DNASequence {

private final static Logger logger = LoggerFactory.getLogger(TranscriptSequence.class);

private final ArrayList<CDSSequence> cdsSequenceList = new ArrayList<>();
private final LinkedHashMap<String, CDSSequence> cdsSequenceHashMap = new LinkedHashMap<>();
private final List<CDSSequence> cdsSequenceList = new ArrayList<>();
private final Map<String, CDSSequence> cdsSequenceHashMap = new LinkedHashMap<>();
private StartCodonSequence startCodonSequence = null;
private StopCodonSequence stopCodonSequence = null;
private GeneSequence parentGeneSequence = null;
Expand Down Expand Up @@ -110,7 +112,7 @@ public CDSSequence removeCDS(String accession) {
* Get the CDS sequences that have been added to the TranscriptSequences
* @return
*/
public LinkedHashMap<String, CDSSequence> getCDSSequences() {
public Map<String, CDSSequence> getCDSSequences() {
return cdsSequenceHashMap;
}

Expand Down Expand Up @@ -152,8 +154,8 @@ public CDSSequence addCDS(AccessionID accession, int begin, int end, int phase)
*
* @return
*/
public ArrayList<ProteinSequence> getProteinCDSSequences() {
ArrayList<ProteinSequence> proteinSequenceList = new ArrayList<>();
public List<ProteinSequence> getProteinCDSSequences() {
List<ProteinSequence> proteinSequenceList = new ArrayList<>();
for (int i = 0; i < cdsSequenceList.size(); i++) {
CDSSequence cdsSequence = cdsSequenceList.get(i);
String codingSequence = cdsSequence.getCodingSequence();
Expand Down
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